This is again the same problem. The fact that when you move the files off one file system into another, it might change the names of the files.
I know, for example, that ntfs stores filenames in utf-16. iTunes xml stores it in utf-8. I’ve been talking with someone else about trying both utf-8 and utf-16 when trying to locate files, and that might solve this specific problem.
I guess we’ll see next nightly.